Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

Appendix B Advanced Topic: Data Analysis Overview
Color-space and base space as applied in the SOLiD 4 System B
Color-space and base space as applied in the
SOLiD 4 System
Color-space data
The final files generated by the SOLiD 4 System are in base space.
To maximize the built-in error correction of 2-base encoding, all file
analysis is conducted in color-space prior to final results.
Rather than reading one base per cycle, the software measures
information on two bases simultaneously. In each cycle, the software
calls one of four colors (color-space call). Because each ligation
measurement event measures two bases, all bases (except for the
final base of a read) are interrogated twice, providing for an
additional level of error correction.
Relationship between cycle and base position
Figure 4 shows the relationship between color-space, base position,
and the sequencing chemistry. Base number refers to base position.
Base 0 is the last base of the adapter and is not part of the target
sequence. The five primer lines show the order in which the data was
generated (0-indexed).
Note: In all files, only processed data refers to a color-space
position.
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